SARS-CoV-2 core polymerase complex inhibited by araCTP

2026-05-27 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Ligand geometry STRUCTURE_SUMMARY atom_site audit_author citation citation_author em_admin em_entity_assembly em_single_particle_entity em_software entity entity_name_com entity_poly entity_poly_seq entity_src_gen ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_contact_author pdbx_database_related pdbx_entity_instance_feature pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly_gen pdbx_struct_conn_angle pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues pdbx_validate_planes pdbx_validate_rmsd_angle pdbx_validate_torsion refine refine_ls_restr struct_asym struct_conf struct_conn struct_mon_prot_cis struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet struct_sheet_order struct_sheet_range _citation.title _em_admin.last_update _em_entity_assembly.entity_id_list _em_entity_assembly.name _entity.formula_weight _entity.pdbx_description _entity.pdbx_ec _entity.pdbx_number_of_molecules _entity_name_com.name _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.pdbx_host_org_scientific_name _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.hbond_type_12 _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _pdbx_contact_author.id _pdbx_struct_assembly_gen.asym_id_list _refine.pdbx_ls_cross_valid_method _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_seq_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_seq_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_seq_id _struct_conf.end_label_asym_id _struct_conf.end_label_comp_id _struct_conf.end_label_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.pdbx_PDB_helix_length _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_omega_angle _struct_ref.db_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.pdbx_db_accession _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end STRUCTURE_SUMMARY citation citation_author em_admin em_entity_assembly em_single_particle_entity em_software entity entity_poly entity_src_gen pdbx_database_related struct_ref struct_ref_seq struct_ref_seq_dif _citation.title _em_admin.last_update _em_entity_assembly.entity_id_list _em_entity_assembly.name _entity.formula_weight _entity.pdbx_description _entity.pdbx_ec _entity.pdbx_number_of_molecules _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.pdbx_end_seq_num _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.pdbx_host_org_scientific_name _struct_ref.db_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.pdbx_db_accession _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end DATA_UPDATED REPOSITORY DATA_UPDATED REPOSITORY DATA_UPDATED REPOSITORY DATA_UPDATED REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update RCSB RCSB 2024-04-30 2025-05-14 2025-05-14 2026-05-27 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI123498 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI158463 United States United States Department of Agriculture (USDA) WIS03099 United States SARS-CoV-2 core polymerase complex inhibited by araCTP Anderson TK Kirchdeorfer RN SARS-CoV-2, RdRP, Polymerase, araCTP, VIRAL PROTEIN, VIRAL PROTEIN-RNA-INHIBITOR complex Xiao Z Das A Jain A Anderson TK Cameron CE Arnold JJ Dulin D Kirchdoerfer RN Incorporation of arabinose-CTP and arabinose-UTP inhibits viral polymerases by inducing long pauses. J.Biol.Chem. US 302 111027 111027 2026 41380964 doi:10.1016/j.jbc.2025.111027 1083-351X 0071 JBCHA3 9blf FULLOVERLAP EMDB EMD-44654 associated EM volume

PDB 9PYW unspecified

SARS-CoV-2 nsp7, nsp8 and nsp12 bound to a primer-template pair with incorporated ara-UMP

PDB 9PZ0 unspecified

SARS-CoV-2 nsp7, nsp8 and nsp12 bound to a primer-template pair

PDB 9PYZ unspecified

SARS-CoV-2 nsp7, nsp8 and nsp12 bound to a primer-template pair with incorporated ara-UMP and UTP

SARS-CoV-2 nsp7, nsp8, nsp12 and an RNA primer-template bound to ara-CMP and ara-CTP SARS-CoV-2 nsp7, nsp8, nsp12 and an RNA primer-template bound to ara-CMP and ara-CTP 0 1 2 3 4 5 Severe acute respiratory syndrome coronavirus 2 0.185 RNA-directed RNA polymerase nsp12 Severe acute respiratory syndrome coronavirus 2 0.110424898 1 Spodoptera frugiperda LEVO MGSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFS NYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFN KKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYY SLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFS TVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSV AALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDK YFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVA GVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVL ARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADK YVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAK CWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYA DVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQENLYFQGSWSHPQFEKGGSGSSWSHP QFEK P0DTD1 Non-structural protein 8 Severe acute respiratory syndrome coronavirus 2 0.021960099999999996 2 Escherichia coli BL21(DE3) LEVO GAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDK RAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQV VDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ P0DTD1 Non-structural protein 7 Severe acute respiratory syndrome coronavirus 2 0.009305854999999998 1 Escherichia coli BL21(DE3) LEVO GSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNR ATLQ P0DTD1 Primer RNA Severe acute respiratory syndrome coronavirus 2 0.009815911 1 CAUUCUCCUAAGAAGCUAUUAAAAUCACAA(CAR) Template RNA synthetic construct 0.012277293 1 AAAAAGGGUUGUGAUUUUAAUAGCUUCUUAGGAGAAUG ZINC ION 6.5409e-05 2 ZN MAGNESIUM ION 2.4305e-05 3 MG 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one 0.000483156 2 HF4 singleParticle particle 4 7.5 50.0 NaCl sodium chloride 25.0 HEPES 2.0 MgCl2 Magnesium Chloride 2.0 dithiothreitol 6.0 CHAPSO EMS Lacey Carbon GOLD 300 GOLD HOLEY GLOW DISCHARGE 20 AIR ETHANE 100 277 FEI VITROBOT MARK IV FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 0.5 2.0 EPU 3.6.0.6389 GATAN K3 BIOQUANTUM (6k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 7UOE C1 3.31 FSC 0.143 CUT-OFF cryoSPARC v4.4.0 158606 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 1 emd_44654.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 272.384 272.384 272.384 90.0 90.0 90.0 X Y Z -1.370122 2.2787266 0.0017365764 0.053589378 1.064 1.064 1.064 0.28 AUTHOR ::::EMDATABANK.org::::EMD-44654:::: emd_44654_msk_1.map emd_44654_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 272.384 272.384 272.384 90.0 90.0 90.0 X Y Z -0.3450246 0.8300742 0.001458626 0.033905737 1.064 1.064 1.064 AUTHOR ::::EMDATABANK.org::::EMD-44654:::: emd_44654_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 272.384 272.384 272.384 90.0 90.0 90.0 X Y Z -0.32801938 0.7661618 0.0014558457 0.0338677 1.064 1.064 1.064 AUTHOR ::::EMDATABANK.org::::EMD-44654::::